Uncovering the hidden (genetic) diversity: Evolutionary processes driving trait selection in microbiomes

Marker genes used in microbiome studies (e.g., 16S rRNA) represent distant evolutionary divergences and thus, these regions are too conserved to detect locally adapted lineages, let alone recent evolutionary change within microbiomes. And while progress has been made in defining microbial species, the high genetic heterogeneity within communities creates inherent issues in delineating populations, the fundamental unit of evolution. To overcome these limitations, we propose the investigation of bacterial ecotypes, defined as highly clustered genotypic and phenotypic strains occupying the same ecological niche. At this resolution, it is possible to identify the traits associated with local adaptation in natural systems.